Getting Started

Getting started

Three ways to run the application

Build	Network use	Typical use
Hosted (https://www.benchside.org)	Loads the page and the plotting library once	Everyday analysis
index.html from a release	Loads the plotting library from its CDN	Version-pinned, archived analyses
benchside-offline.html from a release	None	Air-gapped systems, controlled-access data

All three builds contain identical application code. The offline build additionally embeds Plotly.js 2.32.0.

Minimum inputs

An expression matrix with genes in rows and samples in columns. A design file is optional; without one, groups are inferred from sample names and can be edited before analysis. See Input formats.

The analysis flow

1. Load the matrix, and optionally the design and species annotation.
2. Review the detected settings: design type, normalization, input units and filter.
3. Click Analyze. Every tab is computed from the included samples.
4. Toggle samples in the sample bar to include or exclude them; all results recompute.

For a guided first run with the included demo dataset, follow Tutorial A in the User Guide.